I have a lot of black in my house. I can attest to the fact that black shows every speck of dust. If I had it to do again, I would go with white, cream, gray, or espresso wood surfaces instead of black.

If the carpenter left scrap pieces of wood I would try & stain the scrape piece the color of your gorgeous wood trim. I used a stain that was a stain & a polycoat all-in-one the darkness is determined by the color & how many coats you use. If the carpenter didn't use material that is stainable, then you'll have to paint or leave them natural. In that case I would leave them natural. Black, even w/a gloss coat or not will show absolutely everything as somebody else stated.

I think they look beautiful as is, I'm a big white trim person but your wood tone is very pretty. I have a lot of black and remember dust and black are not good friends if you know what I mean.

PS - I wouldn't paint the back wall of one bookcase and see how it looks with just black shelves and frame. If you don't like it, then paint the entire thing black.

I had a hard time picturing these black, so Google imaged black built-ins and found this:

http://www.andrewsmithwoodworking.com/bookcases.php

So going by this, I think it would look nice. A semi gloss, not flat. I would leave the trim/molding cream however. I also would paint the window frame black to match. These are beautiful built ins by the way as well as the rug.

Search HGTV for "Old World Style 101" to get the guidelines for what you're planning to do. I think their tips will give you direction. Main thing seems to age whatever you paint.
Personally, I think black is too contemporary a color - they usually had wood items that were wood colored back in the day. I would stick to the color of the baseboards and give it an antiqued patina. That would probably mean changing the window trim to match. I think I would have left out the shelf above the window - it is contradicting the nice curve. Looks like it may be an easy removal before you start your painting project!